diff --git a/crates/pet-conda/src/lib.rs b/crates/pet-conda/src/lib.rs
index a444d388..8c3915bd 100644
--- a/crates/pet-conda/src/lib.rs
+++ b/crates/pet-conda/src/lib.rs
@@ -225,24 +225,36 @@ impl Locator for Conda {
         });
 
         match scope {
-            RefreshStateSyncScope::Full => {}
+            RefreshStateSyncScope::Full => {
+                // Full refresh: replace all caches entirely.
+                self.environments.clear();
+                self.environments
+                    .insert_many(source.environments.clone_map());
+
+                self.managers.clear();
+                self.managers.insert_many(source.managers.clone_map());
+
+                self.mamba_managers.clear();
+                self.mamba_managers
+                    .insert_many(source.mamba_managers.clone_map());
+            }
             RefreshStateSyncScope::GlobalFiltered(kind)
-                if self.supported_categories().contains(kind) => {}
-            RefreshStateSyncScope::GlobalFiltered(_) | RefreshStateSyncScope::Workspace => {
-                return;
+                if self.supported_categories().contains(kind) =>
+            {
+                // Filtered refresh: merge discoveries without clearing existing
+                // caches. Today find() exhaustively discovers all conda
+                // environments, but a filtered scope should not assume that and
+                // must not drop entries found by a previous full refresh.
+                // Trade-off: deleted environments may linger until the next Full
+                // refresh, but that is preferable to silently losing live entries.
+                self.environments
+                    .insert_many(source.environments.clone_map());
+                self.managers.insert_many(source.managers.clone_map());
+                self.mamba_managers
+                    .insert_many(source.mamba_managers.clone_map());
             }
+            RefreshStateSyncScope::GlobalFiltered(_) | RefreshStateSyncScope::Workspace => {}
         }
-
-        self.environments.clear();
-        self.environments
-            .insert_many(source.environments.clone_map());
-
-        self.managers.clear();
-        self.managers.insert_many(source.managers.clone_map());
-
-        self.mamba_managers.clear();
-        self.mamba_managers
-            .insert_many(source.mamba_managers.clone_map());
     }
     fn configure(&self, config: &pet_core::Configuration) {
         self.conda_executable
diff --git a/crates/pet-conda/tests/lib_test.rs b/crates/pet-conda/tests/lib_test.rs
index 0afb7d7e..978f9d97 100644
--- a/crates/pet-conda/tests/lib_test.rs
+++ b/crates/pet-conda/tests/lib_test.rs
@@ -3,6 +3,252 @@
 
 mod common;
 
+#[test]
+fn sync_refresh_state_full_replaces_all_caches() {
+    use common::create_test_environment;
+    use pet_conda::Conda;
+    use pet_core::{
+        python_environment::{PythonEnvironment, PythonEnvironmentKind},
+        Locator, RefreshStateSyncScope,
+    };
+    use std::{collections::HashMap, path::PathBuf};
+
+    let env = create_test_environment(HashMap::new(), None, vec![], None);
+    let shared = Conda::from(&env);
+    let transient = Conda::from(&env);
+
+    // Populate shared with two environments from a "previous" refresh.
+    let env_a = PythonEnvironment::new(
+        Some(PathBuf::from("/envs/a/bin/python")),
+        Some(PythonEnvironmentKind::Conda),
+        Some(PathBuf::from("/envs/a")),
+        None,
+        Some("3.10.0".into()),
+    );
+    let env_b = PythonEnvironment::new(
+        Some(PathBuf::from("/envs/b/bin/python")),
+        Some(PythonEnvironmentKind::Conda),
+        Some(PathBuf::from("/envs/b")),
+        None,
+        Some("3.11.0".into()),
+    );
+    shared
+        .environments
+        .insert(PathBuf::from("/envs/a"), env_a.clone());
+    shared
+        .environments
+        .insert(PathBuf::from("/envs/b"), env_b.clone());
+
+    // Transient only discovered env_a (e.g. env_b was deleted).
+    transient
+        .environments
+        .insert(PathBuf::from("/envs/a"), env_a);
+
+    // Full sync should replace: shared loses env_b.
+    shared.sync_refresh_state_from(&transient, &RefreshStateSyncScope::Full);
+
+    assert_eq!(shared.environments.len(), 1);
+    assert!(shared.environments.get(&PathBuf::from("/envs/a")).is_some());
+    assert!(shared.environments.get(&PathBuf::from("/envs/b")).is_none());
+}
+
+#[test]
+fn sync_refresh_state_global_filtered_merges_caches() {
+    use common::create_test_environment;
+    use pet_conda::{manager::CondaManager, Conda};
+    use pet_core::{
+        manager::EnvManagerType,
+        python_environment::{PythonEnvironment, PythonEnvironmentKind},
+        Locator, RefreshStateSyncScope,
+    };
+    use std::{collections::HashMap, path::PathBuf};
+
+    let env = create_test_environment(HashMap::new(), None, vec![], None);
+    let shared = Conda::from(&env);
+    let transient = Conda::from(&env);
+
+    // Populate shared with two environments from a "previous" refresh.
+    let env_a = PythonEnvironment::new(
+        Some(PathBuf::from("/envs/a/bin/python")),
+        Some(PythonEnvironmentKind::Conda),
+        Some(PathBuf::from("/envs/a")),
+        None,
+        Some("3.10.0".into()),
+    );
+    let env_b = PythonEnvironment::new(
+        Some(PathBuf::from("/envs/b/bin/python")),
+        Some(PythonEnvironmentKind::Conda),
+        Some(PathBuf::from("/envs/b")),
+        None,
+        Some("3.11.0".into()),
+    );
+    shared.environments.insert(PathBuf::from("/envs/a"), env_a);
+    shared.environments.insert(PathBuf::from("/envs/b"), env_b);
+
+    // Also populate shared with a manager.
+    let mgr_old = CondaManager {
+        executable: PathBuf::from("/conda/bin/conda"),
+        version: Some("23.0.0".into()),
+        conda_dir: Some(PathBuf::from("/conda")),
+        manager_type: EnvManagerType::Conda,
+    };
+    shared.managers.insert(PathBuf::from("/conda"), mgr_old);
+
+    // Transient discovered env_a (updated) and a new env_c, plus an updated manager.
+    let env_a_updated = PythonEnvironment::new(
+        Some(PathBuf::from("/envs/a/bin/python")),
+        Some(PythonEnvironmentKind::Conda),
+        Some(PathBuf::from("/envs/a")),
+        None,
+        Some("3.10.1".into()),
+    );
+    let env_c = PythonEnvironment::new(
+        Some(PathBuf::from("/envs/c/bin/python")),
+        Some(PythonEnvironmentKind::Conda),
+        Some(PathBuf::from("/envs/c")),
+        None,
+        Some("3.12.0".into()),
+    );
+    transient
+        .environments
+        .insert(PathBuf::from("/envs/a"), env_a_updated);
+    transient
+        .environments
+        .insert(PathBuf::from("/envs/c"), env_c);
+
+    let mgr_new = CondaManager {
+        executable: PathBuf::from("/conda/bin/conda"),
+        version: Some("24.0.0".into()),
+        conda_dir: Some(PathBuf::from("/conda")),
+        manager_type: EnvManagerType::Conda,
+    };
+    transient.managers.insert(PathBuf::from("/conda"), mgr_new);
+
+    // GlobalFiltered(Conda) should merge: shared keeps env_b, updates env_a, adds env_c.
+    shared.sync_refresh_state_from(
+        &transient,
+        &RefreshStateSyncScope::GlobalFiltered(PythonEnvironmentKind::Conda),
+    );
+
+    assert_eq!(shared.environments.len(), 3);
+    assert_eq!(
+        shared
+            .environments
+            .get(&PathBuf::from("/envs/a"))
+            .unwrap()
+            .version,
+        Some("3.10.1".into())
+    );
+    assert!(shared.environments.get(&PathBuf::from("/envs/b")).is_some());
+    assert!(shared.environments.get(&PathBuf::from("/envs/c")).is_some());
+
+    // Manager cache should also be merged (updated, not cleared).
+    assert_eq!(shared.managers.len(), 1);
+    assert_eq!(
+        shared
+            .managers
+            .get(&PathBuf::from("/conda"))
+            .unwrap()
+            .version,
+        Some("24.0.0".into())
+    );
+}
+
+#[test]
+fn sync_refresh_state_full_then_global_filtered_preserves_entries() {
+    use common::create_test_environment;
+    use pet_conda::Conda;
+    use pet_core::{
+        python_environment::{PythonEnvironment, PythonEnvironmentKind},
+        Locator, RefreshStateSyncScope,
+    };
+    use std::{collections::HashMap, path::PathBuf};
+
+    let env = create_test_environment(HashMap::new(), None, vec![], None);
+    let shared = Conda::from(&env);
+
+    // Step 1: Full refresh populates shared with A and B.
+    let transient_full = Conda::from(&env);
+    transient_full.environments.insert(
+        PathBuf::from("/envs/a"),
+        PythonEnvironment::new(
+            Some(PathBuf::from("/envs/a/bin/python")),
+            Some(PythonEnvironmentKind::Conda),
+            Some(PathBuf::from("/envs/a")),
+            None,
+            Some("3.10.0".into()),
+        ),
+    );
+    transient_full.environments.insert(
+        PathBuf::from("/envs/b"),
+        PythonEnvironment::new(
+            Some(PathBuf::from("/envs/b/bin/python")),
+            Some(PythonEnvironmentKind::Conda),
+            Some(PathBuf::from("/envs/b")),
+            None,
+            Some("3.11.0".into()),
+        ),
+    );
+    shared.sync_refresh_state_from(&transient_full, &RefreshStateSyncScope::Full);
+    assert_eq!(shared.environments.len(), 2);
+
+    // Step 2: GlobalFiltered refresh discovers only C; A and B must survive.
+    let transient_filtered = Conda::from(&env);
+    transient_filtered.environments.insert(
+        PathBuf::from("/envs/c"),
+        PythonEnvironment::new(
+            Some(PathBuf::from("/envs/c/bin/python")),
+            Some(PythonEnvironmentKind::Conda),
+            Some(PathBuf::from("/envs/c")),
+            None,
+            Some("3.12.0".into()),
+        ),
+    );
+    shared.sync_refresh_state_from(
+        &transient_filtered,
+        &RefreshStateSyncScope::GlobalFiltered(PythonEnvironmentKind::Conda),
+    );
+
+    assert_eq!(shared.environments.len(), 3);
+    assert!(shared.environments.get(&PathBuf::from("/envs/a")).is_some());
+    assert!(shared.environments.get(&PathBuf::from("/envs/b")).is_some());
+    assert!(shared.environments.get(&PathBuf::from("/envs/c")).is_some());
+}
+
+#[test]
+fn sync_refresh_state_irrelevant_scope_is_noop() {
+    use common::create_test_environment;
+    use pet_conda::Conda;
+    use pet_core::{
+        python_environment::{PythonEnvironment, PythonEnvironmentKind},
+        Locator, RefreshStateSyncScope,
+    };
+    use std::{collections::HashMap, path::PathBuf};
+
+    let env = create_test_environment(HashMap::new(), None, vec![], None);
+    let shared = Conda::from(&env);
+    let transient = Conda::from(&env);
+
+    let env_a = PythonEnvironment::new(
+        Some(PathBuf::from("/envs/a/bin/python")),
+        Some(PythonEnvironmentKind::Conda),
+        Some(PathBuf::from("/envs/a")),
+        None,
+        Some("3.10.0".into()),
+    );
+    shared.environments.insert(PathBuf::from("/envs/a"), env_a);
+
+    // Workspace and unrelated GlobalFiltered should not touch conda caches.
+    shared.sync_refresh_state_from(&transient, &RefreshStateSyncScope::Workspace);
+    assert_eq!(shared.environments.len(), 1);
+
+    shared.sync_refresh_state_from(
+        &transient,
+        &RefreshStateSyncScope::GlobalFiltered(PythonEnvironmentKind::Poetry),
+    );
+    assert_eq!(shared.environments.len(), 1);
+}
+
 #[cfg(unix)]
 #[test]
 fn find_conda_env_without_manager() {